Prenatal iron supplementation is recommended to control anaemia during pregnancy. Low compliance and side effects have been claimed as the main obstacles for adequate impact of the supplementation. As part of a double-blind supplementation study carried out in a hospital located in a shantytown in Lima, Peru, we monitored compliance throughout pregnancy and evaluated factors associated with variation in compliance over time. Overall, 985 pregnant women were enrolled in a supplementation study that was administered through their prenatal care from 10 to 24 weeks of gestation until 4 weeks postpartum. They received 60mg iron and 250μg folate with or without 15mg zinc. Women had monthly care visits and were also visited weekly to query regarding compliance, overall health status, and potential positive and negative effects of supplement consumption. Median compliance was 79% (inter-quartile range: 65-89%) over pregnancy, and the median number of tablets consumed was 106 (81-133). Primpara had lower average compliance; positive health reports were associated with greater compliance, and negative reports were associated with lower compliance. There was no difference by type of supplement. Women with low initial compliance did achieve high compliance by the end of pregnancy, and women who reported forgetting to take the supplements did have lower compliance. Compliance was positively associated with haemoglobin concentration at the end of pregnancy. In conclusion, women comply highly with prenatal supplementation within a prenatal care model in which supplies are maintained and reinforcing messages are provided. © 2012 John Wiley & Sons Ltd.